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Basiru S, Ait Si Mhand K, Hijri M. Disentangling arbuscular mycorrhizal fungi and bacteria at the soil-root interface. MYCORRHIZA 2023; 33:119-137. [PMID: 36961605 DOI: 10.1007/s00572-023-01107-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 02/21/2023] [Indexed: 06/08/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) are essential components of the plant root mycobiome and are found in approximately 80% of land plants. As obligate plant symbionts, AMF harbor their own microbiota, both inside and outside the plant root system. AMF-associated bacteria (AAB) possess various functional traits, including nitrogen fixation, organic and inorganic phosphate mobilization, growth hormone production, biofilm production, enzymatic capabilities, and biocontrol against pathogen attacks, which not only contribute to the health of the arbuscular mycorrhizal symbiosis but also promote plant growth. Because of this, there is increasing interest in the diversity, functioning, and mechanisms that underlie the complex interactions between AMF, AAB, and plant hosts. This review critically examines AMF-associated bacteria, focusing on AAB diversity, the factors driving richness and community composition of these bacteria across various ecosystems, along with the physical, chemical, and biological connections that enable AMF to select and recruit beneficial bacterial symbionts on and within their structures and hyphospheres. Additionally, potential applications of these bacteria in agriculture are discussed, emphasizing the potential importance of AMF fungal highways in engineering plant rhizosphere and endophyte bacteria communities, and the importance of a functional core of AAB taxa as a promising tool to improve plant and soil productivity. Thus, AMF and their highly diverse bacterial taxa represent important tools that could be efficiently explored in sustainable agriculture, carbon sequestration, and reduction of greenhouse gas emissions related to nitrogen fertilizer applications. Nevertheless, future studies adopting integrated multidisciplinary approaches are crucial to better understand AAB functional diversity and the mechanisms that govern these tripartite relationships.
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Affiliation(s)
- Sulaimon Basiru
- African Genome Center, Mohammed VI Polytechnic University (UM6P), Lot 660, Hay Moulay Rachid, Ben Guerir, 43150, Morocco
| | - Khadija Ait Si Mhand
- African Genome Center, Mohammed VI Polytechnic University (UM6P), Lot 660, Hay Moulay Rachid, Ben Guerir, 43150, Morocco
| | - Mohamed Hijri
- African Genome Center, Mohammed VI Polytechnic University (UM6P), Lot 660, Hay Moulay Rachid, Ben Guerir, 43150, Morocco.
- Institut de recherche en biologie végétale (IRBV), Département de Sciences Biologiques, Université de Montréal, QC, Montréal, Canada.
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2
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Liu W, Qiu K, Xie Y, Wang R, Li H, Meng W, Yang Y, Huang Y, Li Y, He Y. Years of sand fixation with Caragana korshinskii drive the enrichment of its rhizosphere functional microbes by accumulating soil N. PeerJ 2022; 10:e14271. [PMID: 36340191 PMCID: PMC9635361 DOI: 10.7717/peerj.14271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 09/28/2022] [Indexed: 11/05/2022] Open
Abstract
C. korshinskii is one of the most widely-planted sand-fixing legumes in northwest China and exploring its rhizosphere microbiome is of great ecological importance. However, the effect of long-term sand fixation on the composition, diversity, and underlying functions of microbes in the C. korshinskii rhizosphere in dryland ecosystems remain unclear. Here, we performed high-throughput sequencing using a 16S rRNA (absolute quantification) and bacterial functional annotation of prokaryotic taxa (FAPROTAX) analysis and an ITS (relative quantification) and fungal functional guild (FUNGuild) analysis to investigate the C. korshinskii rhizosphere microbiome and metabolic functional groups at different sand-fixing ages (six years, CK6; twelve years, CK12; and eighteen years, CK18) and determined the physicochemical properties of the rhizosphere soil. Results showed that the key bacterial taxa of the rhizosphere were significantly more abundant in CK18 than in CK12 and CK6 at the phylum-class-genus level, and that fungal Glomeromycota was also significantly more abundant in the CK18 rhizosphere compared to CK12 and CK6. Among these bacterial taxa, the enrichment effect of key, functional, genus-level species of bacteria was the most obvious, including Rhizobium, Ensifer, Neorhizobium, Mesorhizobium, Streptomyces, Sphingomonas, and Flavobacterium, which are N-fixing and/or phosphate-solubilizing groups. The significant improvement seen in the physicochemical properties of the CK18 rhizosphere soil, including the higher total nitrogen (TN), available nitrogen (AN), pH, electrical conductivity (EC), higher N:P ratio, and lower C:N ratio, all demonstrated the relationship between the rhizosphere microbes and soil carbon (C) and nitrogen (N) cycling. A redundancy analysis (RDA) of different taxonomic levels indicated a close positive relationship between rhizosphere microbes and AN. In addition, the functional groups of the C. korshinskii rhizosphere bacteria were closely related to soil AN and were mainly composed of chemoheterotrophy and aerobic chemoheterotrophy. A Spearman correlation analysis revealed that these functional groups were mainly identified from bacterial Actinobacteria, Proteobacteria, Verrucomicrobia, Bacteroidetes, and fungal Glomeromycota. Our study provides evidence that the rhizosphere microbes of C. korshinskii are closely related to the accumulation of N in the restoration of desert ecosystems, and that the ecological functional processes they are involved in mainly involve C and N cycles, which play an important role in desertification reversal.
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Affiliation(s)
- Wangsuo Liu
- School of Agriculture, Ningxia University, Yinchuan, China,Department of Desertification Prevention, Ningxia Grape Wine and Desertification Prevention Technical College, Yinchuan, Ningxia, China
| | - Kaiyang Qiu
- School of Agriculture, Ningxia University, Yinchuan, China,Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration of Northwest China, Yinchuan, China,Ningxia Grassland and Animal Husbandry Engineering Technology Research Center, Yinchuan, China
| | - Yingzhong Xie
- School of Agriculture, Ningxia University, Yinchuan, China,Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration of Northwest China, Yinchuan, China,Ningxia Grassland and Animal Husbandry Engineering Technology Research Center, Yinchuan, China
| | - Ruixia Wang
- Ningxia Administration of Baijitan National Nature Reserve, Yinchuan, China
| | - Haichao Li
- Ningxia Administration of Baijitan National Nature Reserve, Yinchuan, China
| | - Wenfen Meng
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Yi Yang
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Yeyun Huang
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Yayuan Li
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Yi He
- School of Agriculture, Ningxia University, Yinchuan, China
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3
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Fifani B, Steels S, Helmus C, Delacuvellerie A, Deracinois B, Phalip V, Delvigne F, Jacques P. Coculture of Trichoderma harzianum and Bacillus velezensis Based on Metabolic Cross-Feeding Modulates Lipopeptide Production. Microorganisms 2022; 10:microorganisms10051059. [PMID: 35630500 PMCID: PMC9148127 DOI: 10.3390/microorganisms10051059] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/18/2022] [Accepted: 05/18/2022] [Indexed: 01/27/2023] Open
Abstract
Cocultures have been widely explored for their use in deciphering microbial interaction and its impact on the metabolisms of the interacting microorganisms. In this work, we investigate, in different liquid coculture conditions, the compatibility of two microorganisms with the potential for the biocontrol of plant diseases: the fungus Trichoderma harzianum IHEM5437 and the bacterium Bacillus velezensis GA1 (a strong antifungal lipopeptide producing strain). While the Bacillus overgrew the Trichoderma in a rich medium due to its antifungal lipopeptide production, a drastically different trend was observed in a medium in which a nitrogen nutritional dependency was imposed. Indeed, in this minimum medium containing nitrate as the sole nitrogen source, cooperation between the bacterium and the fungus was established. This is reflected by the growth of both species as well as the inhibition of the expression of Bacillus genes encoding lipopeptide synthetases. Interestingly, the growth of the bacterium in the minimum medium was enabled by the amendment of the culture by the fungal supernatant, which, in this case, ensures a high production yield of lipopeptides. These results highlight, for the first time, that Trichoderma harzianum and Bacillus velezensis are able, in specific environmental conditions, to adapt their metabolisms in order to grow together.
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Affiliation(s)
- Barbara Fifani
- UMR Transfrontalière BioEcoAgro No 1158, University Lille, INRAE, University Liège, UPJV, YNCREA, University Artois, University Littoral Côte d’Opale, TERRA—Teaching and Research Centre, Gembloux Agro-Bio Tech, University Liège, 5030 Gembloux, Belgium; (B.F.); (S.S.); (C.H.); (F.D.)
- UMR Transfrontalière BioEcoAgro No 1158, University Lille, INRAE, University Liège, UPJV, YNCREA, University Artois, University Littoral Côte d’Opale, ICV—Charles Viollette Institute, 59000 Lille, France; (B.D.); (V.P.)
| | - Sebastien Steels
- UMR Transfrontalière BioEcoAgro No 1158, University Lille, INRAE, University Liège, UPJV, YNCREA, University Artois, University Littoral Côte d’Opale, TERRA—Teaching and Research Centre, Gembloux Agro-Bio Tech, University Liège, 5030 Gembloux, Belgium; (B.F.); (S.S.); (C.H.); (F.D.)
| | - Catherine Helmus
- UMR Transfrontalière BioEcoAgro No 1158, University Lille, INRAE, University Liège, UPJV, YNCREA, University Artois, University Littoral Côte d’Opale, TERRA—Teaching and Research Centre, Gembloux Agro-Bio Tech, University Liège, 5030 Gembloux, Belgium; (B.F.); (S.S.); (C.H.); (F.D.)
| | | | - Barbara Deracinois
- UMR Transfrontalière BioEcoAgro No 1158, University Lille, INRAE, University Liège, UPJV, YNCREA, University Artois, University Littoral Côte d’Opale, ICV—Charles Viollette Institute, 59000 Lille, France; (B.D.); (V.P.)
| | - Vincent Phalip
- UMR Transfrontalière BioEcoAgro No 1158, University Lille, INRAE, University Liège, UPJV, YNCREA, University Artois, University Littoral Côte d’Opale, ICV—Charles Viollette Institute, 59000 Lille, France; (B.D.); (V.P.)
| | - Frank Delvigne
- UMR Transfrontalière BioEcoAgro No 1158, University Lille, INRAE, University Liège, UPJV, YNCREA, University Artois, University Littoral Côte d’Opale, TERRA—Teaching and Research Centre, Gembloux Agro-Bio Tech, University Liège, 5030 Gembloux, Belgium; (B.F.); (S.S.); (C.H.); (F.D.)
| | - Philippe Jacques
- UMR Transfrontalière BioEcoAgro No 1158, University Lille, INRAE, University Liège, UPJV, YNCREA, University Artois, University Littoral Côte d’Opale, TERRA—Teaching and Research Centre, Gembloux Agro-Bio Tech, University Liège, 5030 Gembloux, Belgium; (B.F.); (S.S.); (C.H.); (F.D.)
- Correspondence:
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Zhang L, Zhou J, George TS, Limpens E, Feng G. Arbuscular mycorrhizal fungi conducting the hyphosphere bacterial orchestra. TRENDS IN PLANT SCIENCE 2022; 27:402-411. [PMID: 34782247 DOI: 10.1016/j.tplants.2021.10.008] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 10/13/2021] [Accepted: 10/22/2021] [Indexed: 05/22/2023]
Abstract
More than two-thirds of terrestrial plants acquire nutrients by forming a symbiosis with arbuscular mycorrhizal (AM) fungi. AM fungal hyphae recruit distinct microbes into their hyphosphere, the narrow region of soil influenced by hyphal exudates. They thereby shape this so-called second genome of AM fungi, which significantly contributes to nutrient mobilization and turnover. We summarize current insights into characteristics of the hyphosphere microbiome and the role of hyphal exudates on orchestrating its composition. The hyphal exudates not only contain carbon-rich compounds but also promote bacterial growth and activity and influence the microbial community structure. These effects lead to shifts in function and cause changes in organic nutrient cycling, making the hyphosphere a unique and largely overlooked functional zone in ecosystems.
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Affiliation(s)
- Lin Zhang
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193, China
| | - Jiachao Zhou
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193, China
| | | | - Erik Limpens
- Laboratory of Molecular Biology, Wageningen University & Research, Wageningen 6708, PB, The Netherlands
| | - Gu Feng
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193, China.
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5
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Sun N, Jiang F, Zhang L, Feng G. Hyphal exudates of an arbuscular mycorrhizal fungus<italic>Rhizophagus irregularis</italic> induce phosphate-solubilizingbacterium <italic>Rahnella aquatilis</italic> to swim towards its hyphae. CHINESE SCIENCE BULLETIN-CHINESE 2021. [DOI: 10.1360/tb-2021-0579] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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6
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Ujvári G, Turrini A, Avio L, Agnolucci M. Possible role of arbuscular mycorrhizal fungi and associated bacteria in the recruitment of endophytic bacterial communities by plant roots. MYCORRHIZA 2021; 31:527-544. [PMID: 34286366 PMCID: PMC8484141 DOI: 10.1007/s00572-021-01040-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/17/2021] [Indexed: 05/12/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) represent an important group of root symbionts, given the key role they play in the enhancement of plant nutrition, health, and product quality. The services provided by AMF often are facilitated by large and diverse beneficial bacterial communities, closely associated with spores, sporocarps, and extraradical mycelium, showing different functional activities, such as N2 fixation, nutrient mobilization, and plant hormone, antibiotic, and siderophore production and also mycorrhizal establishment promotion, leading to the enhancement of host plant performance. The potential functional complementarity of AMF and associated microbiota poses a key question as to whether members of AMF-associated bacterial communities can colonize the root system after establishment of mycorrhizas, thereby becoming endophytic. Root endophytic bacterial communities are currently studied for the benefits provided to host plants in the form of growth promotion, stress reduction, inhibition of plant pathogens, and plant hormone release. Their quantitative and qualitative composition is influenced by many factors, such as geographical location, soil type, host genotype, and cultivation practices. Recent data suggest that an additional factor affecting bacterial endophyte recruitment could be AMF and their associated bacteria, even though the mechanisms allowing members of AMF-associated bacterial communities to actually establish in the root system, becoming endophytic, remain to be determined. Given the diverse plant growth-promoting properties shown by AMF-associated bacteria, further studies are needed to understand whether AMF may represent suitable tools to introduce beneficial root endophytes in sustainable and organic agriculture where the functioning of such multipartite association may be crucial for crop production.
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Affiliation(s)
- Gergely Ujvári
- Department of Agriculture, Food and Environment, University of Pisa, 56124, Pisa, Italy
| | - Alessandra Turrini
- Department of Agriculture, Food and Environment, University of Pisa, 56124, Pisa, Italy
| | - Luciano Avio
- Department of Agriculture, Food and Environment, University of Pisa, 56124, Pisa, Italy
| | - Monica Agnolucci
- Department of Agriculture, Food and Environment, University of Pisa, 56124, Pisa, Italy.
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Zhang XF, Shi R, Chen M, Zhou XK, Wei YQ, Cha QY, Li N, Su YX, Ma L, Mo MH, Cao Y. Sphingobacterium lumbrici sp. nov., a novel bacterium isolated from wormcast of Eisenia foetida. Int J Syst Evol Microbiol 2021; 71. [PMID: 34047689 DOI: 10.1099/ijsem.0.004823] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative, rod-shaped, non-motile, yellowish bacterium, designated strain 1.3611T, was isolated from the wormcast of Eisenia foetida. The strain grew optimally at 30-37 ℃, at pH 7.0 and with 0-1.0 % (w/v) NaCl. Based on the results of 16S rRNA gene sequence and phylogenetic analyses, strain 1.3611T showed the highest degree of 16S rRNA gene sequence similarity to Sphingobacterium olei HAL-9T (97.0 %), followed by Sphingobacterium alkalisoli Y3L14T (95.8 %). The respiratory quinone of strain 1.3611T was menaquinone-7 (MK-7) and its major cellular fatty acids were iso-C15 : 0 (41.3 %), summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c, 22.1 %) and iso-C17 : 0 3-OH (16.2 %). The major polar lipids were sphingophospholipid, phosphatidylethanolamine, four unidentified glycolipids, two unidentified phospholipids and five unidentified polar lipids. The genomic DNA G+C content was 39.0 mol%. The digital DNA-DNA hybridization and average nucleotide identity values between the genomes of strain 1.3611T and S. olei HAL-9T were 37.9 and 88.9 %, respectively. According to the phenotypic and chemotaxonomic phylogenetic results, strain 1.3611T should represent a novel species of the genus Sphingobacterium, for which the name Sphingobacterium lumbrici sp. nov. is proposed, with strain 1.3611T (=KCTC 62980T=CCTCC AB 2018349T) as the type strain.
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Affiliation(s)
- Xiao-Fei Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, PR China
| | - Rui Shi
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, PR China
| | - Min Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, PR China
| | - Xing-Kui Zhou
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, PR China
| | - Yu-Qian Wei
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, PR China
| | - Qi-Yan Cha
- Kunming Center for Disease Control and Prevention, Kunming, 650228, PR China
| | - Ni Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, PR China
| | - Yuan-Xiao Su
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, PR China
| | - Li Ma
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, PR China
| | - Ming-He Mo
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, PR China
| | - Yi Cao
- Guizhou Academy of Tobacco Science, Guiyang, 550081, PR China
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Wahdan SFM, Heintz-Buschart A, Sansupa C, Tanunchai B, Wu YT, Schädler M, Noll M, Purahong W, Buscot F. Targeting the Active Rhizosphere Microbiome of Trifolium pratense in Grassland Evidences a Stronger-Than-Expected Belowground Biodiversity-Ecosystem Functioning Link. Front Microbiol 2021; 12:629169. [PMID: 33597941 PMCID: PMC7882529 DOI: 10.3389/fmicb.2021.629169] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/08/2021] [Indexed: 12/14/2022] Open
Abstract
The relationship between biodiversity and ecosystem functioning (BEF) is a central issue in soil and microbial ecology. To date, most belowground BEF studies focus on the diversity of microbes analyzed by barcoding on total DNA, which targets both active and inactive microbes. This approach creates a bias as it mixes the part of the microbiome currently steering processes that provide actual ecosystem functions with the part not directly involved. Using experimental extensive grasslands under current and future climate, we used the bromodeoxyuridine (BrdU) immunocapture technique combined with pair-end Illumina sequencing to characterize both total and active microbiomes (including both bacteria and fungi) in the rhizosphere of Trifolium pratense. Rhizosphere function was assessed by measuring the activity of three microbial extracellular enzymes (β-glucosidase, N-acetyl-glucosaminidase, and acid phosphatase), which play central roles in the C, N, and P acquisition. We showed that the richness of overall and specific functional groups of active microbes in rhizosphere soil significantly correlated with the measured enzyme activities, while total microbial richness did not. Active microbes of the rhizosphere represented 42.8 and 32.1% of the total bacterial and fungal taxa, respectively, and were taxonomically and functionally diverse. Nitrogen fixing bacteria were highly active in this system with 71% of the total operational taxonomic units (OTUs) assigned to this group detected as active. We found the total and active microbiomes to display different responses to variations in soil physicochemical factors in the grassland, but with some degree of resistance to a manipulation mimicking future climate. Our findings provide critical insights into the role of active microbes in defining soil ecosystem functions in a grassland ecosystem. We demonstrate that the relationship between biodiversity-ecosystem functioning in soil may be stronger than previously thought.
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Affiliation(s)
- Sara Fareed Mohamed Wahdan
- Department of Soil Ecology, Helmholtz Centre for Environmental Research-UFZ, Halle (Saale), Germany.,Department of Biology, Leipzig University, Leipzig, Germany.,Department of Botany, Faculty of Science, Suez Canal University, Ismailia, Egypt
| | - Anna Heintz-Buschart
- Department of Soil Ecology, Helmholtz Centre for Environmental Research-UFZ, Halle (Saale), Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Chakriya Sansupa
- Department of Soil Ecology, Helmholtz Centre for Environmental Research-UFZ, Halle (Saale), Germany
| | - Benjawan Tanunchai
- Department of Soil Ecology, Helmholtz Centre for Environmental Research-UFZ, Halle (Saale), Germany
| | - Yu-Ting Wu
- Department of Forestry, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Martin Schädler
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.,Department of Community Ecology, Helmholtz Centre for Environmental Research-UFZ, Halle (Saale), Germany
| | - Matthias Noll
- Institute for Bioanalysis, Coburg University of Applied Sciences and Arts, Coburg, Germany
| | - Witoon Purahong
- Department of Soil Ecology, Helmholtz Centre for Environmental Research-UFZ, Halle (Saale), Germany
| | - François Buscot
- Department of Soil Ecology, Helmholtz Centre for Environmental Research-UFZ, Halle (Saale), Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
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9
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Cha QY, Zhou XK, Zhang XF, Li M, Wei YQ, Zhang TK, Qin SC, Liu ZY, Wang XJ, Liu JJ, Zhu ML, Mo MH. Luteimonas lumbrici sp. nov., a novel bacterium isolated from wormcast. Int J Syst Evol Microbiol 2019; 70:604-610. [PMID: 31697229 DOI: 10.1099/ijsem.0.003799] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, yellow-green bacterium, designated 1.1416T, was isolated from wormcast of Eisenia foetida. The strain was non-motile, rod-shaped, and grew optimally on NA medium at 30 °C, pH 7.0 and with 0 % (w/v) NaCl. On the basis of the 16S rRNA gene sequence and phylogenetic analysis, 1.1416T showed the highest degree of 16S rRNA gene sequence similarity to Luteimonas arsenica 26-35T (96.2 %), followed by Luteimonas lutimaris G3T (96.1 %). The respiratory quinone of 1.1416T was ubiquinone-8 (Q-8), and its major cellular fatty acids were iso-C15 : 0 (39.8 %), summed feature 9 (iso-C17 : 1 ω9c or C16 : 0 10-methyl) (18.6 %). The major polar lipids of 1.1416T were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and six unidentified phospholipids. The genomic DNA G+C content of 1.1416T was 71.0 mol%. According to the results of the phenotypic and chemotaxonomic phylogenetic analyses, strain 1.1416T represents a novel species of the genus Luteimonas, for which the name Luteimonas lumbrici sp. nov. is proposed, with strain 1.1416T (=KCTC 62979T=CCTCC AB 2018348T) as the type strain.
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Affiliation(s)
- Qi-Yan Cha
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, PR China
| | - Xing-Kui Zhou
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, PR China
| | - Xiao-Fei Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, PR China
| | - Miao Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, PR China
| | - Yu-Qian Wei
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, PR China
| | - Ti-Kun Zhang
- Yunnan Corporation of China National Tobacco Corporation, Puer 650202, PR China
| | - Shi-Chun Qin
- Yunnan Corporation of China National Tobacco Corporation, Puer 650202, PR China
| | - Zi-Yi Liu
- Yunnan Corporation of China National Tobacco Corporation, Puer 650202, PR China
| | - Xue-Jian Wang
- Yunnan Corporation of China National Tobacco Corporation, Puer 650202, PR China
| | - Jian-Jin Liu
- Yunnan Corporation of China National Tobacco Corporation, Puer 650202, PR China
| | | | - Ming-He Mo
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, PR China.,Biocontrol Engineering Research Center of Crop Disease & Pest, Yunnan Province, Kunming 650091, PR China.,Biocontrol Engineering Research Center of Plant Disease & Pest, Yunnan University, Kunming 650091, PR China
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10
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Couradeau E, Sasse J, Goudeau D, Nath N, Hazen TC, Bowen BP, Chakraborty R, Malmstrom RR, Northen TR. Probing the active fraction of soil microbiomes using BONCAT-FACS. Nat Commun 2019; 10:2770. [PMID: 31235780 PMCID: PMC6591230 DOI: 10.1038/s41467-019-10542-0] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 05/07/2019] [Indexed: 01/17/2023] Open
Abstract
The ability to link soil microbial diversity to soil processes requires technologies that differentiate active microbes from extracellular DNA and dormant cells. Here, we use BONCAT (bioorthogonal non-canonical amino acid tagging) to measure translationally active cells in soils. We compare the active population of two soil depths from Oak Ridge (Tennessee, USA) and find that a maximum of 25-70% of the extractable cells are active. Analysis of 16S rRNA sequences from BONCAT-positive cells recovered by fluorescence-activated cell sorting (FACS) reveals that the phylogenetic composition of the active fraction is distinct from the total population of extractable cells. Some members of the community are found to be active at both depths independently of their abundance rank, suggesting that the incubation conditions favor the activity of similar organisms. We conclude that BONCAT-FACS is effective for interrogating the active fraction of soil microbiomes in situ and provides a new approach for uncovering the links between soil processes and specific microbial groups.
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Affiliation(s)
- Estelle Couradeau
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Joelle Sasse
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Danielle Goudeau
- Joint Genome Institute, Department of Energy, Walnut Creek, CA, USA
| | - Nandita Nath
- Joint Genome Institute, Department of Energy, Walnut Creek, CA, USA
| | - Terry C Hazen
- University of Tennessee, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Ben P Bowen
- Joint Genome Institute, Department of Energy, Walnut Creek, CA, USA
| | - Romy Chakraborty
- Earth Science and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Rex R Malmstrom
- Joint Genome Institute, Department of Energy, Walnut Creek, CA, USA
| | - Trent R Northen
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Joint Genome Institute, Department of Energy, Walnut Creek, CA, USA.
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11
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Mu Y, Zhou X, Liu L, Zhou XK, Zeng XC, Li WJ. Pseudaminobacter arsenicus sp. nov., an arsenic-resistant bacterium isolated from arsenic-rich aquifers. Int J Syst Evol Microbiol 2019; 69:791-797. [PMID: 30676307 DOI: 10.1099/ijsem.0.003238] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An arsenic-resistant strain, CB3T, was isolated from arsenic-rich aquifers at the Jianghan Plain in Hubei, China. Phylogenetic and biochemical analysis suggested that it should represent a new species of the genus Pseudaminobacter in the family Phyllobacteriaceae. The 16S rRNA gene of CB3T shared the highest sequence similarities to those of the type strains Pseudaminobacter defluvii THI 051T (97.8 % identity) and Pseudaminobacter salicylatoxidans BN12T (97.4 %). The DNA-DNA relatedness values of CB3T with respect to strains belonging to the genus Pseudaminobacter were less than 70 %. The fatty acid profile of CB3T consisted of C16 : 0, cyclo-C19 : 0ω8c and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) as major components. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidyldimethylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylethanolamine and diphosphatidylglycerol. The DNA G+C content was 61.4 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain CB3T was distinct from previously described Pseudaminobacter species. Therefore, we propose that strain CB3T represents a novel species of the genus Pseudaminobacter, Pseudaminobacterarsenicus sp. nov., strain CB3T (=CCTCC AB2016116T=KCTC 52625T) is designated as the type strain.
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Affiliation(s)
- Yao Mu
- 1State Key Laboratory of Biogeology and Environmental Geology and Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430074, PR China
| | - Xing Zhou
- 1State Key Laboratory of Biogeology and Environmental Geology and Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430074, PR China
| | - Lan Liu
- 2State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Xing-Kui Zhou
- 3State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, PR China
| | - Xian-Chun Zeng
- 1State Key Laboratory of Biogeology and Environmental Geology and Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430074, PR China
| | - Wen-Jun Li
- 4Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürűmqi 830011, PR China.,2State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
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12
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Molecular and Functional Characterization of Beneficial Bacteria Associated with AMF Spores. METHODS IN RHIZOSPHERE BIOLOGY RESEARCH 2019. [DOI: 10.1007/978-981-13-5767-1_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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13
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Singer E, Wagner M, Woyke T. Capturing the genetic makeup of the active microbiome in situ. THE ISME JOURNAL 2017; 11:1949-1963. [PMID: 28574490 PMCID: PMC5563950 DOI: 10.1038/ismej.2017.59] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 03/02/2017] [Accepted: 03/10/2017] [Indexed: 12/21/2022]
Abstract
More than any other technology, nucleic acid sequencing has enabled microbial ecology studies to be complemented with the data volumes necessary to capture the extent of microbial diversity and dynamics in a wide range of environments. In order to truly understand and predict environmental processes, however, the distinction between active, inactive and dead microbial cells is critical. Also, experimental designs need to be sensitive toward varying population complexity and activity, and temporal as well as spatial scales of process rates. There are a number of approaches, including single-cell techniques, which were designed to study in situ microbial activity and that have been successively coupled to nucleic acid sequencing. The exciting new discoveries regarding in situ microbial activity provide evidence that future microbial ecology studies will indispensably rely on techniques that specifically capture members of the microbiome active in the environment. Herein, we review those currently used activity-based approaches that can be directly linked to shotgun nucleic acid sequencing, evaluate their relevance to ecology studies, and discuss future directions.
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Affiliation(s)
- Esther Singer
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Michael Wagner
- University of Vienna, Department of Microbial Ecology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Tanja Woyke
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
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14
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Margesin R, Siles JA, Cajthaml T, Öhlinger B, Kistler E. Microbiology Meets Archaeology: Soil Microbial Communities Reveal Different Human Activities at Archaic Monte Iato (Sixth Century BC). MICROBIAL ECOLOGY 2017; 73:925-938. [PMID: 27966037 PMCID: PMC5382179 DOI: 10.1007/s00248-016-0904-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 11/24/2016] [Indexed: 06/06/2023]
Abstract
Microbial ecology has been recognized as useful in archaeological studies. At Archaic Monte Iato in Western Sicily, a native (indigenous) building was discovered. The objective of this study was the first examination of soil microbial communities related to this building. Soil samples were collected from archaeological layers at a ritual deposit (food waste disposal) in the main room and above the fireplace in the annex. Microbial soil characterization included abundance (cellular phospholipid fatty acids (PLFA), viable bacterial counts), activity (physiological profiles, enzyme activities of viable bacteria), diversity, and community structure (bacterial and fungal Illumina amplicon sequencing, identification of viable bacteria). PLFA-derived microbial abundance was lower in soils from the fireplace than in soils from the deposit; the opposite was observed with culturable bacteria. Microbial communities in soils from the fireplace had a higher ability to metabolize carboxylic and acetic acids, while those in soils from the deposit metabolized preferentially carbohydrates. The lower deposit layer was characterized by higher total microbial and bacterial abundance and bacterial richness and by a different carbohydrate metabolization profile compared to the upper deposit layer. Microbial community structures in the fireplace were similar and could be distinguished from those in the two deposit layers, which had different microbial communities. Our data confirmed our hypothesis that human consumption habits left traces on microbiota in the archaeological evidence; therefore, microbiological residues as part of the so-called ecofacts are, like artifacts, key indicators of consumer behavior in the past.
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Affiliation(s)
- Rosa Margesin
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria.
| | - José A Siles
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Tomas Cajthaml
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, 142 20, Prague 4, Czech Republic
- Institute for Environmental Studies, Faculty of Science, Charles University in Prague, Benatska 2, 128 01, Prague 2, Czech Republic
| | - Birgit Öhlinger
- Institute of Archaeologies, University of Innsbruck, Langer Weg 11, 6020, Innsbruck, Austria
| | - Erich Kistler
- Institute of Archaeologies, University of Innsbruck, Langer Weg 11, 6020, Innsbruck, Austria
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15
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Guo L, Li T, Tang Y, Yang L, Huo G. Probiotic properties of Enterococcus strains isolated from traditional naturally fermented cream in China. Microb Biotechnol 2016; 9:737-745. [PMID: 26200795 PMCID: PMC5072190 DOI: 10.1111/1751-7915.12306] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 04/16/2015] [Accepted: 06/08/2015] [Indexed: 11/27/2022] Open
Abstract
The purpose of this study was to evaluate the probiotic properties of Enterococcus strains isolated from traditional naturally fermented cream in China. Four Enterococcus isolates showed high cholesterol removal ability in media were identified as Enterococcus durans (KLDS 6.0930 and 6.0933) and Enterococcus faecalis (KLDS 6.0934 and 6.0935) by 16S rRNA and pheS gene sequences, respectively, and selected for further evaluation. In order to assess the probiotic potential and safety of these strains, the property of four Enterococcus strains were examined, including acid and bile tolerance, adherence to Caco-2 cells and antibiotics susceptibility. All four strains showed potential cholesterol assimilation, de-conjugation of bile salts and/or cholesterol degradation to remove cholesterol in vitro. In addition, the potential effect of E. durans KLDS 6.0930 on serum cholesterol levels was evaluated in Sprague-Dawley rats. After 4 weeks administration, compared with rats fed a high-cholesterol diet without lactic acid bacteria supplementation, there was a significant (P < 0.05) decrease in the total cholesterol and low-density lipoprotein cholesterol levels in the serum of rats treated with KLDS 6.0930. Furthermore, total bile acid level in the feces was significantly (P < 0.05) increased after KLDS 6.0930 administration. These observations suggested that the strain E. durans KLDS 6.0930 may be used in the future as a good candidate for lowering human serum cholesterol levels.
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Affiliation(s)
- Lidong Guo
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin, China
- College of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Tingting Li
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Yaru Tang
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Lijie Yang
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin, China
| | - Guicheng Huo
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin, China.
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16
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Genetic Diversity and Association Characters of Bacteria Isolated from Arbuscular Mycorrhizal Fungal Spore Walls. PLoS One 2016; 11:e0160356. [PMID: 27479250 PMCID: PMC4968797 DOI: 10.1371/journal.pone.0160356] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 07/18/2016] [Indexed: 11/19/2022] Open
Abstract
Association between arbuscular mycorrhizal fungi (AMF) and bacteria has long been studied. However, the factors influencing their association in the natural environment is still unknown. This study aimed to isolate bacteria associated with spore walls of AMF and identify their potential characters for association. Spores collected from coastal reclamation land were differentiated based on their morphology and identified by 18S rDNA sequencing as Funneliformis caledonium, Racocetra alborosea and Funneliformis mosseae. Bacteria associated with AMF spore walls were isolated after treating them with disinfection solution at different time intervals. After 0, 10 and 20 min of spore disinfection, 86, 24 and 10 spore associated bacteria (SAB) were isolated, respectively. BOX-PCR fingerprinting analysis showed that diverse bacterial communities were associated to AMF spores. Bacteria belonging to the same genera could associate with different AMF spores. Gram positive bacteria were more closely associated with AMF spores. Isolated SAB were characterized and tested for spore association characters such as chitinase, protease, cellulase enzymes and exopolysaccharide production (EPS). Among the 120 SAB, 113 SAB were able to show one or more characters for association and seven SAB did not show any association characters. The 16S rDNA sequence of SAB revealed that bacteria belonging to the phyla Firmicutes, Proteobacteria, Actinobacteria and Bactereiodes were associated with AMF spore walls.
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17
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Mu Y, Pan Y, Shi W, Liu L, Jiang Z, Luo X, Zeng XC, Li WJ. Luteimonas arsenica sp. nov., an arsenic-tolerant bacterium isolated from arsenic-contaminated soil. Int J Syst Evol Microbiol 2016; 66:2291-2296. [DOI: 10.1099/ijsem.0.001024] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yao Mu
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430074, China
| | - Yunfan Pan
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430074, China
| | - Wanxia Shi
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430074, China
| | - Lan Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Zhao Jiang
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, China
| | - Xuesong Luo
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Xian-Chun Zeng
- State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430074, China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, China
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18
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Benoit I, van den Esker MH, Patyshakuliyeva A, Mattern DJ, Blei F, Zhou M, Dijksterhuis J, Brakhage AA, Kuipers OP, de Vries RP, Kovács ÁT. Bacillus subtilis attachment to Aspergillus niger hyphae results in mutually altered metabolism. Environ Microbiol 2014; 17:2099-113. [PMID: 25040940 DOI: 10.1111/1462-2920.12564] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 07/06/2014] [Indexed: 02/06/2023]
Abstract
Interaction between microbes affects the growth, metabolism and differentiation of members of the microbial community. While direct and indirect competition, like antagonism and nutrient consumption have a negative effect on the interacting members of the population, microbes have also evolved in nature not only to fight, but in some cases to adapt to or support each other, while increasing the fitness of the community. The presence of bacteria and fungi in soil results in various interactions including mutualism. Bacilli attach to the plant root and form complex communities in the rhizosphere. Bacillus subtilis, when grown in the presence of Aspergillus niger, interacts similarly with the fungus, by attaching and growing on the hyphae. Based on data obtained in a dual transcriptome experiment, we suggest that both fungi and bacteria alter their metabolism during this interaction. Interestingly, the transcription of genes related to the antifungal and putative antibacterial defence mechanism of B. subtilis and A. niger, respectively, are decreased upon attachment of bacteria to the mycelia. Analysis of the culture supernatant suggests that surfactin production by B. subtilis was reduced when the bacterium was co-cultivated with the fungus. Our experiments provide new insights into the interaction between a bacterium and a fungus.
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Affiliation(s)
- Isabelle Benoit
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands.,Microbiology, Utrecht University, Utrecht, The Netherlands.,Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands.,Kluyver Centre for Genomics of Industrial Fermentations, Netherlands Genomics Initiative/Netherlands Organization for Scientific Research, Delf, The Netherlands
| | - Marielle H van den Esker
- Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Aleksandrina Patyshakuliyeva
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands.,Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - Derek J Mattern
- Molecular and Applied Microbiology Department, Leibniz Institute for Natural Product Research and Infection Biology - HKI, Jena, Germany.,Department of Microbiology and Molecular Biology, Friedrich Schiller University of Jena, Jena, Germany
| | - Felix Blei
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University of Jena, Jena, Germany
| | - Miaomiao Zhou
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands.,Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - Jan Dijksterhuis
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
| | - Axel A Brakhage
- Molecular and Applied Microbiology Department, Leibniz Institute for Natural Product Research and Infection Biology - HKI, Jena, Germany.,Department of Microbiology and Molecular Biology, Friedrich Schiller University of Jena, Jena, Germany
| | - Oscar P Kuipers
- Kluyver Centre for Genomics of Industrial Fermentations, Netherlands Genomics Initiative/Netherlands Organization for Scientific Research, Delf, The Netherlands.,Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Ronald P de Vries
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands.,Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands.,Kluyver Centre for Genomics of Industrial Fermentations, Netherlands Genomics Initiative/Netherlands Organization for Scientific Research, Delf, The Netherlands
| | - Ákos T Kovács
- Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.,Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University of Jena, Jena, Germany
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19
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David MM, Cecillon S, Warne BM, Prestat E, Jansson JK, Vogel TM. Microbial ecology of chlorinated solvent biodegradation. Environ Microbiol 2014; 17:4835-50. [PMID: 24517489 DOI: 10.1111/1462-2920.12413] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 01/15/2014] [Accepted: 01/26/2014] [Indexed: 01/26/2023]
Abstract
This study focused on the microbial ecology of tetrachloroethene (PCE) degradation to trichloroethene, cis-1,2-dichloroethene and vinyl chloride to evaluate the relationship between the microbial community and the potential accumulation or degradation of these toxic metabolites. Multiple soil microcosms supplied with different organic substrates were artificially contaminated with PCE. A thymidine analogue, bromodeoxyuridine (BrdU), was added to the microcosms and incorporated into the DNA of actively replicating cells. We compared the total and active bacterial communities during the 50-day incubations by using phylogenic microarrays and 454 pyrosequencing to identify microorganisms and functional genes associated with PCE degradation to ethene. By use of this integrative approach, both the key community members and the ecological functions concomitant with complete PCE degradation could be determined, including the presence and activity of microbial community members responsible for producing hydrogen and acetate, which are critical for Dehalococcoides-mediated PCE degradation. In addition, by correlation of chemical data and phylogenic microarray data, we identified several bacteria that could potentially oxidize hydrogen. These results demonstrate that PCE degradation is dependent on some microbial community members for production of appropriate metabolites, while other members of the community compete for hydrogen in soil at low redox potentials.
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Affiliation(s)
- Maude M David
- Environmental Microbial Genomics group, Laboratoire Ampère, CNRS UMR 5005, Ecole Centrale de Lyon, Université de Lyon, 36 avenue Guy de Collongue, Ecully, 69134, France.,Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sebastien Cecillon
- Environmental Microbial Genomics group, Laboratoire Ampère, CNRS UMR 5005, Ecole Centrale de Lyon, Université de Lyon, 36 avenue Guy de Collongue, Ecully, 69134, France
| | - Brett M Warne
- Massachussets Institute of Technology, Cambridge, MA, USA
| | - Emmanuel Prestat
- Environmental Microbial Genomics group, Laboratoire Ampère, CNRS UMR 5005, Ecole Centrale de Lyon, Université de Lyon, 36 avenue Guy de Collongue, Ecully, 69134, France
| | - Janet K Jansson
- Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Timothy M Vogel
- Environmental Microbial Genomics group, Laboratoire Ampère, CNRS UMR 5005, Ecole Centrale de Lyon, Université de Lyon, 36 avenue Guy de Collongue, Ecully, 69134, France
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20
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Neu TR, Lawrence JR. Investigation of microbial biofilm structure by laser scanning microscopy. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2014; 146:1-51. [PMID: 24840778 DOI: 10.1007/10_2014_272] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Microbial bioaggregates and biofilms are hydrated three-dimensional structures of cells and extracellular polymeric substances (EPS). Microbial communities associated with interfaces and the samples thereof may come from natural, technical, and medical habitats. For imaging such complex microbial communities confocal laser scanning microscopy (CLSM) is the method of choice. CLSM allows flexible mounting and noninvasive three-dimensional sectioning of hydrated, living, as well as fixed samples. For this purpose a broad range of objective lenses is available having different working distance and resolution. By means of CLSM the signals detected may originate from reflection, autofluorescence, reporter genes/fluorescence proteins, fluorochromes binding to specific targets, or other probes conjugated with fluorochromes. Recorded datasets can be used not only for visualization but also for semiquantitative analysis. As a result CLSM represents a very useful tool for imaging of microbiological samples in combination with other analytical techniques.
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Affiliation(s)
- Thomas R Neu
- Department of River Ecology, Helmholtz Centre for Environmental Research-UFZ, Brueckstrasse 3a, 39114, Magdeburg, Germany,
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21
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Bravo D, Martin G, David MM, Cailleau G, Verrecchia E, Junier P. Identification of active oxalotrophic bacteria by Bromodeoxyuridine DNA labeling in a microcosm soil experiments. FEMS Microbiol Lett 2013; 348:103-11. [PMID: 24033776 DOI: 10.1111/1574-6968.12244] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 08/19/2013] [Accepted: 08/26/2013] [Indexed: 11/30/2022] Open
Abstract
The oxalate-carbonate pathway (OCP) leads to a potential carbon sink in terrestrial environments. This process is linked to the activity of oxalotrophic bacteria. Although isolation and molecular characterizations are used to study oxalotrophic bacteria, these approaches do not give information on the active oxalotrophs present in soil undergoing the OCP. The aim of this study was to assess the diversity of active oxalotrophic bacteria in soil microcosms using the Bromodeoxyuridine (BrdU) DNA labeling technique. Soil was collected near an oxalogenic tree (Milicia excelsa). Different concentrations of calcium oxalate (0.5%, 1%, and 4% w/w) were added to the soil microcosms and compared with an untreated control. After 12 days of incubation, a maximal pH of 7.7 was measured for microcosms with oxalate (initial pH 6.4). At this time point, a DGGE profile of the frc gene was performed from BrdU-labeled soil DNA and unlabeled soil DNA. Actinobacteria (Streptomyces- and Kribbella-like sequences), Gammaproteobacteria and Betaproteobacteria were found as the main active oxalotrophic bacterial groups. This study highlights the relevance of Actinobacteria as members of the active bacterial community and the identification of novel uncultured oxalotrophic groups (i.e. Kribbella) active in soils.
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Affiliation(s)
- Daniel Bravo
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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22
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Jansa J, Bukovská P, Gryndler M. Mycorrhizal hyphae as ecological niche for highly specialized hypersymbionts - or just soil free-riders? FRONTIERS IN PLANT SCIENCE 2013; 4:134. [PMID: 23720665 PMCID: PMC3655320 DOI: 10.3389/fpls.2013.00134] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 04/22/2013] [Indexed: 05/23/2023]
Abstract
Mycorrhizal fungi interconnect two different kinds of environments, namely the plant roots with the surrounding soil. This widespread coexistence of plants and fungi has important consequences for plant mineral nutrition, water acquisition, carbon allocation, tolerance to abiotic and biotic stresses and interplant competition. Yet some current research indicates a number of important roles to be played by hyphae-associated microbes, in addition to the hyphae themselves, in foraging for and acquisition of soil resources and in transformation of organic carbon in the soil-plant systems. We critically review the available scientific evidence for the theory that the surface of mycorrhizal hyphae in soil is colonized by highly specialized microbial communities, and that these fulfill important functions in the ecology of mycorrhizal fungal hyphae such as accessing recalcitrant forms of mineral nutrients, and production of signaling and other compounds in the vicinity of the hyphae. The validity of another hypothesis will then be addressed, namely that the specific associative microbes are rewarded with exclusive access to fungal carbon, which would qualify them as hypersymbionts (i.e., symbionts of symbiotic mycorrhizal fungi). Thereafter, we ask whether recruitment of functionally different microbial assemblages by the hyphae is required under different soil conditions (questioning what evidence is available for such an effect), and we identify knowledge gaps requiring further attention.
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Affiliation(s)
- Jan Jansa
- Department of Ecology, Institute of Microbiology, Academy of Sciences of the Czech RepublicPraha, Czech Republic
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Nuccio EE, Hodge A, Pett-Ridge J, Herman DJ, Weber PK, Firestone MK. An arbuscular mycorrhizal fungus significantly modifies the soil bacterial community and nitrogen cycling during litter decomposition. Environ Microbiol 2013; 15:1870-81. [DOI: 10.1111/1462-2920.12081] [Citation(s) in RCA: 214] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2012] [Revised: 12/16/2012] [Accepted: 12/27/2012] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | | | - Peter K. Weber
- Lawrence Livermore National Laboratory; Livermore; CA; USA
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Yates MD, Kiely PD, Call DF, Rismani-Yazdi H, Bibby K, Peccia J, Regan JM, Logan BE. Convergent development of anodic bacterial communities in microbial fuel cells. ISME JOURNAL 2012; 6:2002-13. [PMID: 22572637 PMCID: PMC3475369 DOI: 10.1038/ismej.2012.42] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Microbial fuel cells (MFCs) are often inoculated from a single wastewater source. The extent that the inoculum affects community development or power production is unknown. The stable anodic microbial communities in MFCs were examined using three inocula: a wastewater treatment plant sample known to produce consistent power densities, a second wastewater treatment plant sample, and an anaerobic bog sediment. The bog-inoculated MFCs initially produced higher power densities than the wastewater-inoculated MFCs, but after 20 cycles all MFCs on average converged to similar voltages (470±20 mV) and maximum power densities (590±170 mW m−2). The power output from replicate bog-inoculated MFCs was not significantly different, but one wastewater-inoculated MFC (UAJA3 (UAJA, University Area Joint Authority Wastewater Treatment Plant)) produced substantially less power. Denaturing gradient gel electrophoresis profiling showed a stable exoelectrogenic biofilm community in all samples after 11 cycles. After 16 cycles the predominance of Geobacter spp. in anode communities was identified using 16S rRNA gene clone libraries (58±10%), fluorescent in-situ hybridization (FISH) (63±6%) and pyrosequencing (81±4%). While the clone library analysis for the underperforming UAJA3 had a significantly lower percentage of Geobacter spp. sequences (36%), suggesting that a predominance of this microbe was needed for convergent power densities, the lower percentage of this species was not verified by FISH or pyrosequencing analyses. These results show that the predominance of Geobacter spp. in acetate-fed systems was consistent with good MFC performance and independent of the inoculum source.
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Affiliation(s)
- Matthew D Yates
- Department of Civil and Environmental Engineering, The Pennsylvania State University, University Park, PA 16802, USA
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25
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Hrynkiewicz K, Dabrowska G, Baum C, Niedojadlo K, Leinweber P. Interactive and Single Effects of Ectomycorrhiza Formation and Bacillus cereus on Metallothionein MT1 Expression and Phytoextraction of Cd and Zn by Willows. WATER, AIR, AND SOIL POLLUTION 2012; 223:957-968. [PMID: 22389535 PMCID: PMC3283765 DOI: 10.1007/s11270-011-0915-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Accepted: 08/03/2011] [Indexed: 05/24/2023]
Abstract
Single and joint ectomycorrhizal (+ Hebeloma mesophaeum) and bacterial (+ Bacillus cereus) inoculations of willows (Salix viminalis) were investigated for their potential and mode of action in the promotion of cadmium (Cd) and zinc (Zn) phytoextraction. Dual fungal and bacterial inoculations promoted the biomass production of willows in contaminated soil. Single inoculations either had no effect on the plant growth or inhibited it. All inoculated willows showed increased concentrations of nutritional elements (N, P, K and Zn) and decreased concentrations of Cd in the shoots. The lowest biomass production and concentration of Cd in the willows (+ B. cereus) were combined with the strongest expression of metallothioneins. It seems that biotic stress from bacterial invasion increased the synthesis of these stress proteins, which responded in decreased Cd concentrations. Contents of Cd and Zn in the stems of willows were combination-specific, but were always increased in dual inoculated plants. In conclusion, single inoculations with former mycorrhiza-associated B. cereus strains decreased the phytoextraction efficiency of willows by causing biotic stress. However, their joint inoculation with an ectomycorrhizal fungus is a very promising method for promoting the phytoextraction of Cd and Zn through combined physiological effects on the plant.
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Affiliation(s)
- Katarzyna Hrynkiewicz
- Soil Science, University of Rostock, Justus-von-Liebig-Weg 6, 18059 Rostock, Germany
- Department of Microbiology, Institute of General and Molecular Biology, N. Copernicus University of Torun, Torun, Poland
| | - Grazyna Dabrowska
- Department of Genetics, Institute of General and Molecular Biology, N. Copernicus University of Torun, Torun, Poland
| | - Christel Baum
- Soil Science, University of Rostock, Justus-von-Liebig-Weg 6, 18059 Rostock, Germany
| | - Katarzyna Niedojadlo
- Department of Cell Biology, Institute of General and Molecular Biology, N. Copernicus University of Torun, Torun, Poland
| | - Peter Leinweber
- Soil Science, University of Rostock, Justus-von-Liebig-Weg 6, 18059 Rostock, Germany
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26
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Miransari M. Soil microbes and plant fertilization. Appl Microbiol Biotechnol 2011; 92:875-85. [PMID: 21989562 DOI: 10.1007/s00253-011-3521-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Revised: 07/08/2011] [Accepted: 07/28/2011] [Indexed: 10/17/2022]
Abstract
With respect to the adverse effects of chemical fertilization on the environment and their related expenses, especially when overused, alternative methods of fertilization have been suggested and tested. For example, the combined use of chemical fertilization with organic fertilization and/or biological fertilization is among such methods. It has been indicated that the use of organic fertilization with chemical fertilization is a suitable method of providing crop plants with adequate amount of nutrients, while environmentally and economically appropriate. In this article, the importance of soil microbes to the ecosystem is reviewed, with particular emphasis on the role of plant growth-promoting rhizobacteria, arbuscular mycorrhizal fungi, and endophytic bacteria in providing necessary nutrients for plant growth and yield production. Such microbes are beneficial to plant growth through colonizing plant roots and inducing mechanisms by which plant growth increases. Although there has been extensive research work regarding the use of microbes as a method of fertilizing plants, it is yet a question how the efficiency of such microbial fertilization to the plant can be determined and increased. In other words, how the right combination of chemical and biological fertilization can be determined. In this article, the most recent advances regarding the effects of microbial fertilization on plant growth and yield production in their combined use with chemical fertilization are reviewed. There are also some details related to the molecular mechanisms affecting the microbial performance and how the use of biological techniques may affect the efficiency of biological fertilization.
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Affiliation(s)
- Mohammad Miransari
- Department of Soil Science, College of Agricultural Sciences, Shahed University, Tehran 18151/159, Iran.
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27
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Taniguchi A, Tada Y, Hamasaki K. Seasonal variations in the community structure of actively growing bacteria in neritic waters of Hiroshima Bay, western Japan. Microbes Environ 2011; 26:339-46. [PMID: 21791885 DOI: 10.1264/jsme2.me11212] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Using bromodeoxyuridine (BrdU) magnetic beads immunocapture and a PCR-denaturing gradient gel electrophoresis (DGGE) technique (BUMP-DGGE), we determined seasonal variations in the community structures of actively growing bacteria in the neritic waters of Hiroshima Bay, western Japan. The community structures of actively growing bacteria were separated into two clusters, corresponding to the timing of phytoplankton blooms in the autumn-winter and spring-summer seasons. The trigger for changes in bacterial community structure was related to organic matter supply from phytoplankton blooms. We identified 23 phylotypes of actively growing bacteria, belonging to Alphaproteobacteria (Roseobacter group, 9 phylotypes), Gammaproteobacteria (2 phylotypes), Bacteroidetes (8 phylotypes), and Actinobacteria (4 phylotypes). The Roseobacter group and Bacteroidetes were dominant in actively growing bacterial communities every month, and together accounted for more than 70% of the total DGGE bands. We revealed that community structures of actively growing bacteria shifted markedly in the wake of phytoplankton blooms in the neritic waters of Hiroshima Bay.
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Affiliation(s)
- Akito Taniguchi
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
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Survey of bromodeoxyuridine uptake among environmental bacteria and variation in uptake rates in a taxonomically diverse set of bacterial isolates. J Microbiol Methods 2011; 86:376-8. [PMID: 21663771 DOI: 10.1016/j.mimet.2011.05.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Revised: 05/23/2011] [Accepted: 05/26/2011] [Indexed: 11/23/2022]
Abstract
Incorporation of 5-Bromo-2'-Deoxyuridine (BrdU) into DNA can be used to target replicating bacteria in the environment, but differential uptake capacity is a potential bias. Among 23 bacterial isolates commonly found in soils, most took up BrdU, but at up to 10-fold different cell-specific rates. Combined with results from an in silico analysis of 1000 BrdU-labeled 16S rRNA gene sequences, our results demonstrate a BrdU uptake bias with no apparent relationship between taxa affiliation and ability to incorporate BrdU.
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29
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Goldfarb KC, Karaoz U, Hanson CA, Santee CA, Bradford MA, Treseder KK, Wallenstein MD, Brodie EL. Differential growth responses of soil bacterial taxa to carbon substrates of varying chemical recalcitrance. Front Microbiol 2011; 2:94. [PMID: 21833332 PMCID: PMC3153052 DOI: 10.3389/fmicb.2011.00094] [Citation(s) in RCA: 232] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Accepted: 04/18/2011] [Indexed: 02/01/2023] Open
Abstract
Soils are immensely diverse microbial habitats with thousands of co-existing bacterial, archaeal, and fungal species. Across broad spatial scales, factors such as pH and soil moisture appear to determine the diversity and structure of soil bacterial communities. Within any one site however, bacterial taxon diversity is high and factors maintaining this diversity are poorly resolved. Candidate factors include organic substrate availability and chemical recalcitrance, and given that they appear to structure bacterial communities at the phylum level, we examine whether these factors might structure bacterial communities at finer levels of taxonomic resolution. Analyzing 16S rRNA gene composition of nucleotide analog-labeled DNA by PhyloChip microarrays, we compare relative growth rates on organic substrates of increasing chemical recalcitrance of >2,200 bacterial taxa across 43 divisions/phyla. Taxa that increase in relative abundance with labile organic substrates (i.e., glycine, sucrose) are numerous (>500), phylogenetically clustered, and occur predominantly in two phyla (Proteobacteria and Actinobacteria) including orders Actinomycetales, Enterobacteriales, Burkholderiales, Rhodocyclales, Alteromonadales, and Pseudomonadales. Taxa increasing in relative abundance with more chemically recalcitrant substrates (i.e., cellulose, lignin, or tannin–protein) are fewer (168) but more phylogenetically dispersed, occurring across eight phyla and including Clostridiales, Sphingomonadalaes, Desulfovibrionales. Just over 6% of detected taxa, including many Burkholderiales increase in relative abundance with both labile and chemically recalcitrant substrates. Estimates of median rRNA copy number per genome of responding taxa demonstrate that these patterns are broadly consistent with bacterial growth strategies. Taken together, these data suggest that changes in availability of intrinsically labile substrates may result in predictable shifts in soil bacterial composition.
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Affiliation(s)
- Katherine C Goldfarb
- Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
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30
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Leigh J, Fitter AH, Hodge A. Growth and symbiotic effectiveness of an arbuscular mycorrhizal fungus in organic matter in competition with soil bacteria. FEMS Microbiol Ecol 2011; 76:428-38. [PMID: 21303398 DOI: 10.1111/j.1574-6941.2011.01066.x] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Arbuscular mycorrhizal (AM) fungi can enhance the rate of decomposition of organic material, and can acquire nitrogen (N) from organic sources, although they are not saprotrophs. These fungi may instead indirectly influence decomposition through interactions with other soil microorganisms. We investigated the impact of both AM hyphae and a bacterial filtrate on N capture by a host plant from sterilized organic material (Lolium perenne shoots dual labelled with (15) N and (13) C), using compartmented microcosms. The addition of a bacterial filtrate considerably suppressed AM hyphal growth in the patch and reduced the root phosphorus content, demonstrating that bacterial populations can reduce symbiotic effectiveness. In contrast, AM hyphae had only a limited impact on bacterial community structure. Uptake of (15) N greatly exceeded that of (13) C, demonstrating that fungi acquired N in an inorganic form. We also examined the ability of AM fungi in gnotobiotic hairy root culture to acquire N directly from organic materials of varying complexities (glutamic acid, urea, bacterial lysate and L. perenne shoots). AM colonization did not enhance root N capture from these materials, although the bacterial lysate reduced both total AM colonization and arbuscule frequency. Collectively, these data demonstrate antagonistic interactions between AM fungi and bacteria that reflect resource competition for decomposition products.
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Affiliation(s)
- Joanne Leigh
- Department of Biology, University of York, Heslington, York, UK
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31
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Izumi H, Finlay RD. Ectomycorrhizal roots select distinctive bacterial and ascomycete communities in Swedish subarctic forests. Environ Microbiol 2010; 13:819-30. [PMID: 21176055 DOI: 10.1111/j.1462-2920.2010.02393.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Ectomycorrhizal (ECM) roots represent important niches for interactions with bacteria and ascomycete fungi, since they have a large surface area and receive a direct supply of plant assimilates from their tree hosts. We tested the hypothesis that the roots colonized by specific ECM fungi harbour distinct bacteria/ascomycete communities. Roots were collected from two different locations in a subarctic shrub forest dominated by Betula pubescens. Bacterial and ascomycete communities were analysed by PCR-DGGE and sequencing, in roots colonized by five frequently observed ECM fungi, Leccinum variicolor, Piloderma fallax, Tomentellopsis submollis, Lactarius torminosus and Pseudotomentella tristis. The bacterial communities associated with P. fallax- or P. tristis-colonized roots were distinct from those associated with roots colonized by three other ECM fungi at both sampling locations. Bacterial communities associated with T. submollis-, L. torminosus- and L. variicolor-colonized roots were more similar to each other. Lactarius- and Pseudotomentella-colonized roots hosted distinct ascomycete communities at one site while only the community associated with Lactarius was distinct at the second location. The results thus suggest that while the community structure of bacteria colonizing ECM roots can be influenced by the local soil environment, there can also be a strong selective effect of particular fungal symbionts.
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Affiliation(s)
- Hironari Izumi
- Uppsala BioCenter, Department of Forest Mycology & Pathology, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden.
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32
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Pushing the limits for amplifying BrdU-labeled DNA encoding 16S rRNA: DNA polymerase as the determining factor. J Microbiol Methods 2010; 83:312-6. [PMID: 20883730 DOI: 10.1016/j.mimet.2010.09.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2010] [Revised: 09/14/2010] [Accepted: 09/19/2010] [Indexed: 11/24/2022]
Abstract
Identifying microorganisms that are active under specific conditions in ecosystems is a challenge in microbial ecology. Recently, the bromodeoxyuridine (BrdU) technique was developed to label actively growing cells. BrdU, a thymidine analog, is incorporated into newly synthesized DNA, and the BrdU-labeled DNA is then isolated from total extractable DNA by immunocapture using a BrdU-specific antibody. Analyzing the BrdU-labeled DNA allows for assessing the actively growing community, which can then be compared to the unlabeled DNA that represents the total community. However, applying the BrdU approach to study soils has been problematic due to low DNA amounts and soil contaminants. To address these challenges, we developed a protocol, optimizing specificity and reproducibility, to amplify BrdU-labeled gene fragments encoding 16S rRNA. We found that the determining factor was the DNA polymerase: among the 13 different polymerases we tested, only 3 provided adequate yields with minimal contamination, and only two of those three produced similar amplification patterns of community DNA.
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33
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Scheublin TR, Sanders IR, Keel C, van der Meer JR. Characterisation of microbial communities colonising the hyphal surfaces of arbuscular mycorrhizal fungi. ISME JOURNAL 2010; 4:752-63. [PMID: 20147983 DOI: 10.1038/ismej.2010.5] [Citation(s) in RCA: 118] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Arbuscular mycorrhizal fungi (AMF) are symbiotic soil fungi that are intimately associated with the roots of the majority of land plants. They colonise the interior of the roots and the hyphae extend into the soil. It is well known that bacterial colonisation of the rhizosphere can be crucial for many pathogenic as well as symbiotic plant-microbe interactions. However, although bacteria colonising the extraradical AMF hyphae (the hyphosphere) might be equally important for AMF symbiosis, little is known regarding which bacterial species would colonise AMF hyphae. In this study, we investigated which bacterial communities might be associated with AMF hyphae. As bacterial-hyphal attachment is extremely difficult to study in situ, we designed a system to grow AMF hyphae of Glomus intraradices and Glomus proliferum and studied which bacteria separated from an agricultural soil specifically attach to the hyphae. Characterisation of attached and non-attached bacterial communities was performed using terminal restriction fragment length polymorphism and clone library sequencing of 16S ribosomal RNA (rRNA) gene fragments. For all experiments, the composition of hyphal attached bacterial communities was different from the non-attached communities, and was also different from bacterial communities that had attached to glass wool (a non-living substratum). Analysis of amplified 16S rRNA genes indicated that in particular bacteria from the family of Oxalobacteraceae were highly abundant on AMF hyphae, suggesting that they may have developed specific interactions with the fungi.
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Affiliation(s)
- Tanja R Scheublin
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.
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34
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Microscopic detection of viable Staphylococcus epidermidis in peri-implant tissue in experimental biomaterial-associated infection, identified by bromodeoxyuridine incorporation. Infect Immun 2010; 78:954-62. [PMID: 20048041 DOI: 10.1128/iai.00849-09] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Infection of biomedical devices is characterized by biofilm formation and colonization of surrounding tissue by the causative pathogens. To investigate whether bacteria detected microscopically in tissue surrounding infected devices were viable, we used bromodeoxyuridine (BrdU), a nucleotide analogue that is incorporated into bacterial DNA and can be detected with antibodies. Infected human tissue was obtained postmortem from patients with intravascular devices, and mouse biopsy specimens were obtained from mice with experimental biomaterial infection. In vitro experiments showed that Staphylococcus epidermidis incorporated BrdU, as judged from staining of the bacteria with anti-BrdU antibodies. After incubation of bacteria with BrdU and subsequent staining of microscopic sections with anti-BrdU antibodies, bacteria could be clearly visualized in the tissue surrounding intravascular devices of deceased patients. With this staining technique, relapse of infection could be visualized in mice challenged with a low dose of S. epidermidis and treated with dexamethasone between 14 and 21 days after challenge to suppress immunity. This confirms and extends our previous findings that pericatheter tissue is a reservoir for bacteria in biomaterial-associated infection. The pathogenesis of the infection and temporo-spatial distribution of viable, dividing bacteria can now be studied at the microscopic level by immunolabeling with BrdU and BrdU antibodies.
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35
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Johansson JF, Paul LR, Finlay RD. Microbial interactions in the mycorrhizosphere and their significance for sustainable agriculture. FEMS Microbiol Ecol 2009; 48:1-13. [PMID: 19712426 DOI: 10.1016/j.femsec.2003.11.012] [Citation(s) in RCA: 306] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
In sustainable, low-input cropping systems the natural roles of microorganisms in maintaining soil fertility and biocontrol of plant pathogens may be more important than in conventional agriculture where their significance has been marginalised by high inputs of agrochemicals. Better understanding of the interactions between arbuscular mycorrhizal fungi and other microorganisms is necessary for the development of sustainable management of soil fertility and crop production. Many studies of the influence of mycorrhizal colonisation on associated bacterial communities have been conducted, however, the mechanisms of interaction are still poorly understood. Novel approaches including PCR-based methods, stable isotope profiling, and molecular markers have begun to shed light on the activity, identity and spatiotemporal location of bacteria in the mycorrhizosphere. This paper reviews current knowledge concerning the interactions between arbuscular mycorrhizal fungi and other microorganisms, particularly bacteria, and discusses the implications these interactions may have in sustainable agriculture.
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Affiliation(s)
- Jonas F Johansson
- Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
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36
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Closing the Global Energy and Nutrient Cycles through Application of Biogas Residue to Agricultural Land – Potential Benefits and Drawback. ENERGIES 2009. [DOI: 10.3390/en20200226] [Citation(s) in RCA: 184] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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37
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Yamahara KM, Walters SP, Boehm AB. Growth of enterococci in unaltered, unseeded beach sands subjected to tidal wetting. Appl Environ Microbiol 2009; 75:1517-24. [PMID: 19151188 PMCID: PMC2655449 DOI: 10.1128/aem.02278-08] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2008] [Accepted: 01/06/2009] [Indexed: 11/20/2022] Open
Abstract
Enterococci are indicator bacteria used to assess the risk of acquiring enteric disease from swimming in marine waters. Previous work identified beach sands as reservoirs of enterococci which can be transported from the sand to the sea, where they may instigate beach advisories. The present study establishes that naturally occurring enterococci can replicate in beach sands under environmentally relevant conditions. In unseeded, nonsterile microcosm experiments, it was shown that intermittent wetting of sands by seawater, like that which would occur at the high tide line, stimulates the transient replication of enterococci at rates of 0.20 to 0.63 per day (equivalent to doubling times of 1.1 to 3.5 days). Replication was not observed in control microcosms that were not subjected to wetting. Enterococci were enumerated using both culture-dependent (membrane filtration and mEI media) and culture-independent (quantitative PCR [QPCR], 23S rRNA gene based) techniques, which allowed tracking of both culturable and total enterococcus populations. Inhibition of QPCR and DNA extraction efficiencies were accounted for in the interpretation of the QPCR results. The results provide evidence that enterococci may not be an appropriate indicator of enteric disease risk at recreational beaches subject to nonpoint sources of pollution.
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Affiliation(s)
- Kevan M Yamahara
- Department of Civil and Environmental Engineering, Environmental and Water Studies, Stanford University, Stanford, CA 94305-4020, USA
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38
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Jäderlund L, Arthurson V, Granhall U, Jansson JK. Specific interactions between arbuscular mycorrhizal fungi and plant growth-promoting bacteria: as revealed by different combinations. FEMS Microbiol Lett 2008; 287:174-80. [DOI: 10.1111/j.1574-6968.2008.01318.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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39
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Arthurson V. Proper sanitization of sewage sludge: a critical issue for a sustainable society. Appl Environ Microbiol 2008; 74:5267-75. [PMID: 18606792 PMCID: PMC2546642 DOI: 10.1128/aem.00438-08] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Veronica Arthurson
- Department of Microbiology, Swedish University of Agricultural Sciences, Box 7025, 75007 Uppsala, Sweden.
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40
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Edlund A, Jansson JK. Use of bromodeoxyuridine immunocapture to identify psychrotolerant phenanthrene-degrading bacteria in phenanthrene-enriched polluted Baltic Sea sediments. FEMS Microbiol Ecol 2008; 65:513-25. [DOI: 10.1111/j.1574-6941.2008.00513.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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41
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42
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Edlund A, Hårdeman F, Jansson JK, Sjöling S. Active bacterial community structure along vertical redox gradients in Baltic Sea sediment. Environ Microbiol 2008; 10:2051-63. [PMID: 18452546 DOI: 10.1111/j.1462-2920.2008.01624.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Community structures of active bacterial populations were investigated along a vertical redox profile in coastal Baltic Sea sediments by terminal-restriction fragment length polymorphism (T-RFLP) and clone library analysis. According to correspondence analysis of T-RFLP results and sequencing of cloned 16S rRNA genes, the microbial community structures at three redox depths (179, -64 and -337 mV) differed significantly. The bacterial communities in the community DNA differed from those in bromodeoxyuridine (BrdU)-labelled DNA, indicating that the growing members of the community that incorporated BrdU were not necessarily the most dominant members. The structures of the actively growing bacterial communities were most strongly correlated to organic carbon followed by total nitrogen and redox potentials. Bacterial identification by sequencing of 16S rRNA genes from clones of BrdU-labelled DNA and DNA from reverse transcription polymerase chain reaction showed that bacterial taxa involved in nitrogen and sulfur cycling were metabolically active along the redox profiles. Several sequences had low similarities to previously detected sequences, indicating that novel lineages of bacteria are present in Baltic Sea sediments. Also, a high number of different 16S rRNA gene sequences representing different phyla were detected at all sampling depths.
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Affiliation(s)
- Anna Edlund
- Södertörn University College, School of Life Sciences, SE-141 89 Huddinge, Sweden
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43
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Scupham AJ. Examination of the microbial ecology of the avian intestine in vivo using bromodeoxyuridine. Environ Microbiol 2008; 9:1801-9. [PMID: 17564613 DOI: 10.1111/j.1462-2920.2007.01300.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Bromodeoxyuridine, a thymidine analogue that can be incorporated into the DNA of actively dividing cells, has been used in vivo to identify intestinal bacteria that are metabolically active in 3-week-old turkey poults during an acute period of feed withdrawal. Automated ribosomal intergenic spacer analysis was used to identify amplicons unique to animals subjected to feed withdrawal. One amplicon was unique to fasted birds while two amplicons were present in 60% of fasted birds and absent in all fed birds. Sequence analysis of 16S ribosomal genes indicated the caecal communities of all birds were dominated by Clostridiaceae while also harbouring low levels of metabolically active gamma-proteobacteria and Bacteroides. Twenty per cent of clones from the fasted animals were identified as belonging to the genus Papillibacter, suggesting these microbes may be specifically dividing in response to environmental conditions present in the caeca of fasted birds.
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Affiliation(s)
- Alexandra J Scupham
- Pre-Harvest Food Safety and Enteric Diseases Research Unit, National Animal Disease Center, USDA, Agricultural Research Service, Ames, IA 50010, USA.
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Taniguchi A, Hamasaki K. Community structures of actively growing bacteria shift along a north-south transect in the western North Pacific. Environ Microbiol 2007; 10:1007-17. [PMID: 18177366 PMCID: PMC2327212 DOI: 10.1111/j.1462-2920.2007.01521.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Bacterial community structures and their activities in the ocean are tightly coupled with organic matter fluxes and thus control ocean biogeochemical cycles. Bromodeoxyuridine (BrdU), halogenated nucleoside and thymidine analogue, has been recently used to monitor actively growing bacteria (AGB) in natural environments. We labelled DNA of proliferating cells in seawater bacterial assemblages with BrdU and determined community structures of the bacteria that were possible key species in mediating biochemical reactions in the ocean. Surface seawater samples were collected along a north-south transect in the North Pacific in October 2003 and subjected to BrdU magnetic beads immunocapture and PCR-DGGE (BUMP-DGGE) analysis. Change of BrdU-incorporated community structures reflected the change of water masses along a north-south transect from subarctic to subtropical gyres in the North Pacific. We identified 25 bands referred to AGB as BrdU-incorporated phylotypes, belonging to Alphaproteobacteria (5 bands), Betaproteobacteria (1 band), Gammaproteobacteria (4 bands), Cytophaga-Flavobacterium-Bacteroides (CFB) group bacteria (5 bands), Gram-positive bacteria (6 bands), and Cyanobacteria (4 bands). BrdU-incorporated phylotypes belonging to Vibrionales, Alteromonadales and Gram-positive bacteria appeared only at sampling stations in a subtropical gyre, while those belonging to Roseobacter-related bacteria and CFB group bacteria appeared at the stations in both subarctic and subtropical gyres. Our result revealed phylogenetic affiliation of AGB and their dynamic change along with north-south environmental gradients in open oceans. Different species of AGB utilize different amount and kinds of substrates, which can affect the change of organic matter fluxes along transect.
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Affiliation(s)
- Akito Taniguchi
- Graduate School of Biosphere Science, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima, Hiroshima, Japan.
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Purin S, Rillig MC. Parasitism of arbuscular mycorrhizal fungi: reviewing the evidence. FEMS Microbiol Lett 2007; 279:8-14. [PMID: 18070075 DOI: 10.1111/j.1574-6968.2007.01007.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
In order to understand the functioning of mycorrhizal fungi in ecosystems it is necessary to consider the full suite of possible biotic interactions in the soil. While a number of such interactions have recently been shown to be crucially important, parasitism is a highly neglected feature in the ecology of arbuscular mycorrhizal fungi (AMF). A number of studies have classified some interactions between populations of bacteria and fungi with AMF as parasitism, generating discussion about its consequences at both 'parasite' and host population levels. This paper reviews these various publications, and based on a set of criteria that are necessary to demonstrate parasitism, it was concluded that parasitism has not been conclusively shown to exist in AMF, even though some data are highly suggestive of such a relationship. The difficulties in gathering data supportive of parasitism were discussed, and hypotheses for defense were offered. This paper concludes by presenting potential consequences of AMF parasitism at the population/community levels and by discussing applied aspects.
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Affiliation(s)
- Sonia Purin
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV 26506-6108, USA.
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In situ activity of suspended and immobilized microbial communities as measured by fluorescence lifetime imaging. Appl Environ Microbiol 2007; 74:294-9. [PMID: 17981940 DOI: 10.1128/aem.01806-07] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this study, the feasibility of fluorescence lifetime imaging (FLIM) for measurement of RNA:DNA ratios in microorganisms was assessed. The fluorescence lifetime of a nucleic acid-specific probe (SYTO 13) was used to directly measure the RNA:DNA ratio inside living bacterial cells. In vitro, SYTO 13 showed shorter fluorescence lifetimes in DNA solutions than in RNA solutions. Growth experiments with bacterial monocultures were performed in liquid media. The results demonstrated the suitability of SYTO 13 for measuring the growth-phase-dependent RNA:DNA ratio in Escherichia coli cells. The fluorescence lifetime of SYTO 13 reflected the known changes of the RNA:DNA ratio in microbial cells during different growth phases. As a result, the growth rate of E. coli cells strongly correlated with the fluorescence lifetime. Finally, the fluorescence lifetimes of SYTO 13 in slow- and fast-growing biofilms were compared. For this purpose, biofilms developed from activated sludge were grown as autotrophic and heterotrophic communities. The FLIM data clearly showed a longer fluorescence lifetime for the fast-growing heterotrophic biofilms and a shorter fluorescence lifetime for the slow-growing autotrophic biofilms. Furthermore, starved biofilms showed shorter lifetimes than biofilms supplied with glucose, indicating a lower RNA:DNA ratio in starved biofilms. It is suggested that FLIM in combination with SYTO 13 represents a useful tool for the in situ differentiation of active and inactive bacteria. The technique does not require radioactive chemicals and may be applied to a broad range of sample types, including suspended and immobilized microorganisms.
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Seneviratne G, Zavahir JS, Bandara WMMS, Weerasekara MLMAW. Fungal-bacterial biofilms: their development for novel biotechnological applications. World J Microbiol Biotechnol 2007. [DOI: 10.1007/s11274-007-9539-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Mou X, Hodson RE, Moran MA. Bacterioplankton assemblages transforming dissolved organic compounds in coastal seawater. Environ Microbiol 2007; 9:2025-37. [PMID: 17635547 DOI: 10.1111/j.1462-2920.2007.01318.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To characterize bacterioplankton functional assemblages that transform specific components of the coastal seawater dissolved organic carbon (DOC) pool, bromodeoxyuridine (BrdU) was used to label the bacterioplankton cells that were active following addition of single-DOC model compounds: two organic osmolytes [dimethylsulfoniopropionate (DMSP) and glycine betaine (GlyB)] and two aromatic monomers [para-hydroxybenzoic acid (pHBA) and vanillic acid (VanA)]. Bacterial populations were analysed based on in situ fluorescent immunodetection of BrdU incorporation followed by fluorescence-activated cell sorting (FACS). Sorted cells were then characterized by 16S rDNA-based analysis. Populations with high BrdU incorporation level (HI) developed within 8 h of introduction of 100 nM model compound. Terminal restriction fragment length polymorphisms (T-RFLP) analysis indicated that the HI populations in all four amendments were composed of bacteria from the same major taxa (phylum and subphylum levels), but the relative abundance of each differed. High-resolution clone libraries (each containing approximately 200 clones) showed that the HI populations in the GlyB and VanA amendments consisted of both metabolic generalists and specialists within the alpha-Proteobacteria (mainly members of the Roseobacter clade), beta-Proteobacteria and gamma-Proteobacteria (mainly members of Altermonadaceae, Chromatiaceae, Oceanospirillaceae and Pseudomonadaceae). The presence of members of OM60/241, OM185, SAR11, SAR86 and SAR116 in the HI populations indicated that members of these groups can assimilate the model DOC compounds, providing some of the first glimpses into heterotrophy by members of these poorly understood environmental clusters.
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Affiliation(s)
- Xiaozhen Mou
- Department of Marine Sciences, University of Georgia, Athens, GA 30602, USA
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Hjort K, Lembke A, Speksnijder A, Smalla K, Jansson JK. Community structure of actively growing bacterial populations in plant pathogen suppressive soil. MICROBIAL ECOLOGY 2007; 53:399-413. [PMID: 16944345 DOI: 10.1007/s00248-006-9120-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2006] [Accepted: 05/01/2006] [Indexed: 05/11/2023]
Abstract
The bacterial community in soil was screened by using various molecular approaches for bacterial populations that were activated upon addition of different supplements. Plasmodiophora brassicae spores, chitin, sodium acetate, and cabbage plants were added to activate specific bacterial populations as an aid in screening for novel antagonists to plant pathogens. DNA from growing bacteria was specifically extracted from the soil by bromodeoxyuridine immunocapture. The captured DNA was fingerprinted by terminal restriction fragment length polymorphism (T-RFLP). The composition of the dominant bacterial community was also analyzed directly by T-RFLP and by denaturing gradient gel electrophoresis (DGGE). After chitin addition to the soil, some bacterial populations increased dramatically and became dominant both in the total and in the actively growing community. Some of the emerging bands on DGGE gels from chitin-amended soil were sequenced and found to be similar to known chitin-degrading genera such as Oerskovia, Kitasatospora, and Streptomyces species. Some of these sequences could be matched to specific terminal restriction fragments on the T-RFLP output. After addition of Plasmodiophora spores, an increase in specific Pseudomonads could be observed with Pseudomonas-specific primers for DGGE. These results demonstrate the utility of microbiomics, or a combination of molecular approaches, for investigating the composition of complex microbial communities in soil.
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Affiliation(s)
- Karin Hjort
- Department of Microbiology, Swedish University of Agricultural Sciences, Box 7025, SE-750 07, Uppsala, Sweden
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Hamasaki K, Taniguchi A, Tada Y, Long RA, Azam F. Actively growing bacteria in the inland sea of Japan, identified by combined bromodeoxyuridine immunocapture and denaturing gradient gel electrophoresis. Appl Environ Microbiol 2007; 73:2787-98. [PMID: 17337555 PMCID: PMC1892868 DOI: 10.1128/aem.02111-06] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A fundamental question in microbial oceanography concerns the relationship between prokaryote diversity and biogeochemical function in an ecosystem context. We combined bromodeoxyuridine (BrdU) magnetic bead immunocapture and PCR-denaturing gradient gel electrophoresis (BUMP-DGGE) to examine phylotype-specific growth in natural marine assemblages. We also examined a broad range of marine bacterial isolates to determine their abilities to incorporate BrdU in order to test the validity of the method for application to diverse marine assemblages. We found that 27 of 29 isolates belonging to different taxa could incorporate BrdU. BUMP-DGGE analysis revealed phylogenetic affiliations of DNA-synthesizing, presumably actively growing bacteria across a eutrophic to mesotrophic transect in the Inland Sea of Japan. We found that the BrdU-incorporating (growing) communities were substantially different from the total communities. The majority (34/56) of phylotypes incorporated BrdU and were presumably growing, and these phylotypes comprised 10 alphaproteobacteria, 1 betaproteobacterium, 11 gammaproteobacteria, 11 Cytophaga-Flavobacterium-Bacteroides group bacteria, and 1 unclassified bacterium. All BrdU-responsive alphaproteobacteria were members of the Rhodobacterales, suggesting that such bacteria were dominant in the growing alphaproteobacterial populations in our samples. The BrdU-responsive gammaproteobacteria belonged to the Oceanospirillales, the SAR86 cluster, the Pseudomonadales, the Alteromonadales, and the Vibrionales. Thus, contemporaneous cooccurrence of diverse actively growing bacterial taxa was a consistent pattern in our biogeochemically varied study area.
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Affiliation(s)
- Koji Hamasaki
- Graduate School of Biosphere Science, Hiroshima University, Hiroshima, Japan.
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